Major Graphic Enhancement

One of the issue that has arisen with the features on the site increasing is difficulty finding items later. A second issue is making things clearer for the non-technical person to understand if there is or is not an issue. If you are on the far left or far right of any of these chart — there is likely an issue.

I have just pushed an uber-page up which will display over 280 potential measures on microbiome samples — all measures are shown on charts with the values of other people who have shared their samples. If you are logged on, your values will be shown on the charts. All of these charts are on the same page, http://microbiomeprescription.azurewebsites.net/library/Distribution , but they contain different types of data.

I also switched to log(values) for the charts because of some extreme values. The key issue is not the number, but where you are compared to other samples. Using a log does not alter that.

At the top of the page you can select WHAT you wish to look at, and which sample.

Conditions

Just select the condition that you are interested in.

My sample when the ME/CFS relapse started. Earlier I was much further the left.

End Products

This is a count of the bacteria that produces various end products. The information is incomplete (list is here).

Low of end product has been associated with ME/CFS

uBiome Metabolites

This is an artifact set of charts from those that transcribed they data from uBiome. Their “1.0” for reference samples is totally suspect. These charts should indicate if you have an abnormal amount (far left or right).

Bacteria Ratios

I have included two ratios (and may add more upon request).

Taxa Counts in Reports

This was done earlier as ‘Quality of Sample’. It also gives an indication on the number of bacteria test for by various companies

Clearly, Thryve tests for more bacteria!

Bottom Line

There are a lot of charts but they are consolidated on one page with the ability to just scroll down and look at your sample values for each.

Bacteria Changers have increased

A reader reported a bug with the manual selection of which taxa to modify page that I did a while back. As a result, I smoothed the flow; I also realized that I need to allow a wider search for modifiers since the bacteria selected may have few known modifiers from studies– especially when a species or strain is selected.
Site: http://microbiomeprescription.azurewebsites.net/

Quick Recap on how to Manual Select bacteria taxa

This is done via the “My Biome View” button from the Samples Page

On this page, you can select which taxa you wish to have included in the suggestions. You make the choices entirely.

Click the button and you will return to the Sample Page and a new button will appear:

This takes you to the usual custom suggestion page (except most of the bacteria filters are hidden — after all, you have hand picked them!)

Note the new choices with emojis!

Parent and children Modifiers are being added

Bacteria is reported in a hierarchy, the next level up is the parent, the next level down are the childern

Above you see that the Parent of Oscillibacter is Oscillospiraceae. Things reported to modify the parent will likely modify its children. The key work is likely. A modifier may reduce Marseillibacter but not Oscillibacter; we lack the studies.

Similarly, the three children of Oscillibacter may have items that modify them. One would expect that if something reduces one of the children then Oscillibacter would be reduced too! Again the key word is likely.

On the Reference pages for Bacteria, you will now see three icons

IF we have 10 or more modifier documented to change this bacteria, we do not include the parent or the children. If we have less than 10 then we include this additional information (giving it a reduced weight reflecting the greater uncertainty).

On some bacteria you may see the same items from all three levels!

Bottom Line

Do not ask me what is the right way to get suggestions. We do not know. What I can provide are tools that will generate suggestions is a logical manner. This latest addition extends the prior choices by:

  • Allowing you to hand pick the taxa from your sample, one by one
  • Allows you to extend the list of modifiers by asking to include items that modify its children (i.e. Lactobacillus Fermentum CQPC04 modifiers would be added to Lactobacillus Fermentum , OR/and its parent (i.e. Lactobacillus) if we have sparse information on how to modify it.

I expect only a few people will make use of this; but it is there if you want absolute control.

Gluten Consuming Bacteria

I have a regular task of manual reviewing potential studies selected by Textural Analysis (Artificial Intelligence/Data Science) published on PubMed. The count of articles reviewed by the AI and myself (for those that the AI selected) is up to 456,847 with many more to go. One of these articles listed the bacteria identified by this study (from human samples) that consumes/process gluten.

It is logical to hypothesis that gluten intolerance/issues is connected to the absence/low numbers of these bacterias.

Diversity of the cultivable human gut microbiome involved in gluten metabolism: isolation of microorganisms with potential interest for coeliac disease. MS Microbiol Ecol. 2014 May;88(2):309-19.

I have added these facts to my website and created a new entry under End Products.

I do not have (in reality) any issues with gluten, and at 37%ile, I would not expect any.

Bottom Line

This is an experimental page. I am curious to see what people with mild to severe gluten issues report their readings to be.

If you are gluten intolerance and wish to see it this explanation actually fits, I would suggest a 16s analysis of your microbiome. With the death of uBiome, Thryve offers the best “bang” (most taxa reported – 500-1200 different bacteria often) for the cost ($ < $100).

Microbiome Shifts Reduces Symptoms in ME/CFS

The 2018 study, “Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons.” reports symptoms improvements with increases and decreases of certain bacteria associated with ME/CFS.

A reader asks me to do a recap of what the known shifts are, and thus what you wish to try to correct (and not inadvertently increase by the wrong supplements, probiotics or diet choices).

In terms of published studies, I have assembled a dynamic list on my website (not verified and subject to data entry errors) shown below for genus level and above. When an item is repeated on multiple lines, this means that we have multiple studies report it. H-High, L- Low, B- High or Low (outside of normal)

It is unlikely that every ME/CFS will have all of these shifts. Most will have some.

At the Strain Level, we also have a long list,

Remember, for Low, it is not uncommon for people to have none of these and be perfectly healthy. The Low count is from the average of the group in the study and not definitive for any individual.

Using the citizen science aspect of my site, we do not have a information based on physician verification of precise clinical definition but solely on self-reporting of symptoms. If click on one of the above, say Bifidobacterium, we see two things listed:

  • Citizen Science discoveries dealing with symptoms.
  • Published studies listing conditions that may have the same shift (thus, potential conditions that ME/CFS may evolve to).

For 1 (EBV),2 (MCS), 4(Female), 5, 6 (Post exertional malaise) are in the list of items that are used for a ME/CFS diagnosis

Going over to Faecalibacterium (3 citations) – another LOW one, we see a more massive symptom list, many many are in the classic ME/CFS diagnosis list.

Doing another one, Streptococcus – a HIGH one for a change (3 citations – 2 high and 1 low), we see

Double Validation

One list of bacteria comes from studies on patients that conform to strict definitions of ME/CFS. The other list of bacteria comes out of the symptoms people self-report and their 16s microbiome results. We have a very strong agreement with the results coming from two independent approaches.

What does this mean?

It means that altering the microbiome will improve symptoms (as indicated in the study cited at the start; and in personal agreement with my own experience and many of my readers).

The next step is to determine which of these long lists of bacteria is involved with your ME/CFS/IBS etc. The old conventional tests only does a few of the bacteria — and do not cover all of those reported in studies. By old conventional tests, I mean:

A 16s report is strongly recommended (choices). Thryve offers the best “bang” (most taxa reported – 500-1200 different bacteria often) for the cost ($ < $100). Many 16s tests are sold direct to consumers and do not require going thru a physician (Just like DNA tests, for example 23andMe).

Once you know the bacteria involved, you need to know how to change them. If your physician, nutritionist or other health professional are well skilled and read on the microbiome, they should be able to guide you.

If they are not, I have created my free analysis and suggestion artificial intelligence engine http://microbiomeprescription.azurewebsites.net/ which uses over 95,000 medical facts on the microbiome. You must review those suggestions with your medical profession because some may be inappropriate given other medical conditions.

Candida – What Studies Find

The Candida species play a role in a healthy body. It is when there is too many that problems start. A friend asked me to put together what we know based on published studies only, no urban-medical-beliefs.

  • There is an increased total fungal load particularly of Candida and Malassezia species in the faeces and mucosa of Crohn’s disease patients, and a lower fungal diversity in the faeces of ulcerative colitis patients. [2019]

Herbs

Antifungal efficacy of herbs (2019). The larger the numbers above, the more effective it is

So to translate into familiar terms, in decreasing effectiveness:

  • Garlic vine ( Echinophora platybola )
  • Benth ( Pogostemon parviflorus )
  • Ashwagandha (Withania somnifera) – Easy to get
  • Turmeric (Curcuma longa) – Easy to get
  • Asthma-plant (Ayurveda- Euphorbia hirta )
  • Ginger (Zingiber officinale )
  • Henna ( Lawsonia inermis )
  • Swertia ( Ayurveda – Swertia chirata )

These are cited, with further studies on this page (in french) and includes the above with links to multiple additional studies for each.

Other Stuff

  • ” It can be concluded that monolaurin has a potential antifungal activity against C. albicans and can modulate the pro-inflammatory response of the host. ” [2016]
  • ” The difference between the groups [chlorhexidine, lactobacillus probiotics, coconut oil] was not statistically significant (Chi-square value 7.42, P value 0.06). ” [2016]
  • ” Eucommia ulmoides, Polygonum cuspidatum, Poria cocos and Uncaria rhyncophylla showed activity against both bacterial and fungal strains, indicating their broad spectrum of activity. ” [2013]
  • ” Data show that mustard [i.e. Turmeric] and coconut oil seem to be effective as in these the spore germination was poor. ” 1992
  • Pau D’Arco ( Tabebuia ) – Studies found no significant effect [1994]
    • Tabebuia avellanedae (methanol extract), with MIC varying from 0.06 to 0.001 mg/mL;  ” [2010] – this is a fraction of the effectiveness of items above.

Probiotics

  • Enterococcus Faecalis appears effective [2014] (available as probiotic)
  • Lactobacillus GG, Lactobacillus rhamnosus LC705 and Propionibacterium freudenreichii ssp. shermanii JS was shown to be an effective means of controlling oral Candida and hypo‐salivation in the elderly (Hatakka et al2007). [2016]
  • Bacillus subtilis exhibited clear zones of inhibition for Candida albicans and Candida parapsilosis but not for Candida krusei. [2016]

Sookkhee et al., in 2001, studied the effects on Candida albicans growth of different lactic-acid bacteria isolated from the oral cavity of volunteers and found that two strains, Lactobacillus paracasei and Lactobacillus rhamnosus, had the strongest effect on the yeast [44].
Lactobacillus reuteri is a promising bacterium (especially DSM 17938 and ATCC PTA 5289) for its anti-Candida properties, confirmed by several studies. In one of these, Lactobacillus reuteri was demonstrated to be able to reduce Candida load in vivo through co-aggregation, modification of oral pH with production of lactic acid and other organic acids that inhibit the virulence of Candida cells, and production of H2O2 [45].
In a recent in vitro study by Coman et al. (2014), the strains Lactobacillus rhamnosus IMC 501 and lactobacillus paracasei IMC 502, alone or in combination, showed an inhibitory effect on Candida spp. growth [46].
Lactobacillus delbrueckii ssp. bulgaricus B1 and Lactobacillus delbrueckii ssp. bulgaricus TAB2 were found to fight Candida, releasing high amounts of lactic acid [47].Recently, it was found that Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 modulate Candida glabrata virulence, through the complete inhibition of fungal biofilms [48].In addition, Lactobacillus acidophilus ATCC 4356 was found to inhibit the biofilm formation of fungus through in vitro experiments [49]. Biofilm formation is probably reduced through the production of substances called “bacteriocins” by probiotics. Wannun et al. reported the isolation of a bacteriocin, called “fermencin SD11”, from Lactobacillus fermentum SD11, a human oral Lactobacillus, which has a strong inhibitory effect on oral Candida cells [50].

Effect of Probiotics on Oral Candidiasis: A Systematic Review and Meta-Analysis 2019

Histamine Caution

  • All Lactobacillus Reuteri are histamine producers.
  • Many Bacillus subtilis are histamine producers [2007]

Lactobacillus rhamnosus appears not to be a histamine producer and reduces histamines [2011]